T CELL RECEPTORS AND ENGINEERED CELLS EXPRESSING SAME

• US 20190321401A1
• Filed: 04/03/2019
• Published: 10/24/2019
• Est. Priority Date: 04/05/2018
• Status: Active Grant

• Current Assignee: Juno Therapeutics Incorporated (Bristol-Myers Squibb Company)
• Original Assignee: Juno Therapeutics Incorporated (Bristol-Myers Squibb Company)
• Inventors: GOLDFLESS, Stephen Jacob, BELMONT, Brian, BRANDT, Cameron, CROFT, Alexandra, HUSS, David Jeffrey
• Granted Patent: US 11,471,489 B2
• Time in Patent Office: Days
• CPC Class Codes: A61K 2239/31 characterized by the route of administration
• CPC Class Codes: A61K 2239/38 characterised by the dose, timing or administration schedule
• CPC Class Codes: A61K 2239/46 characterised by the cancer treated
• CPC Class Codes: A61K 35/17 Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes when activated by a specific antigen A61K39/00
• CPC Class Codes: A61K 39/4611 T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
• CPC Class Codes: A61K 39/4632 T-cell receptors [TCR]; antibody T-cell receptor constructs
• CPC Class Codes: A61K 39/4644 Cancer antigens
• CPC Class Codes: A61K 39/464838 Viral antigens
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/025 Papovaviridae, e.g. papillomavirus, polyomavirus, SV40, BK virus, JC virus
• CPC Class Codes: C07K 14/7051 T-cell receptor (TcR)-CD3 complex
• CPC Class Codes: C07K 16/084 Papovaviridae, e.g. papillomavirus, polyomavirus, SV40, BK virus, JC virus
• CPC Class Codes: C07K 16/2833 against MHC-molecules, e.g. HLA-molecules
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 5/0636 T lymphocytes

Abstract

Provided herein are binding molecules, such as those that recognize or bind a peptide epitope of a cancer antigen, such as expressed on a cancer cell, including cells infected with human papilloma virus (HPV) or that contain HPV DNA sequences and/or those that recognize or bind a peptide epitope of HPV 16 E6 or E7, in the context of a major histocompatibility complex (MHC) molecule. Among the provided binding molecules are T cell receptors (TCRs) or antibodies, including antigen-binding fragments thereof, that bind or recognize such peptide epitopes. The present disclosure further relates to engineered cells comprising such binding molecules, e.g., TCRs or antibodies (and chimeric antigen receptors containing the antibodies), and uses thereof in adoptive cell therapy.

Claims

1-157. -157. (canceled)

158. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Va) region and a beta chain comprising a variable beta (Vβ

) region, wherein;

the Vα

region comprises a complementarity determining region 1 (CDR-1), a complementarity determining region 2 (CDR-2), and a complementarity determining region 3 (CDR-3), comprising the amino acid sequences of SEQ ID NOs;

48, 49, and 50, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

61, 62, and 63, respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

78, 79, and 80, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

89, 90, and 91, respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

104, 105, and 106, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

89, 90, and 115, respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

127, 128, and 129, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

89, 90, and 138, respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

127, 128, and 150, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

89, 90, and 158, respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

170, 171, and 172, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

181, 182, and 183 respectively;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

196, 197, and 198, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

207, 208, and 209, respectively;

or

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

222, 223, and 224, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

233, 234, and 235, respectively.

159. The T cell receptor (TCR) or antigen-binding fragment thereof of claim 158, wherein:

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

47 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

60, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

77 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

88, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

103 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

114, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

126 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

137, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

149 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

157, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

169 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

180, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

195 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

206, or an amino acid sequence that has at least 90% sequence identity thereto;

or

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

221 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

232, or an amino acid sequence that has at least 90% sequence identity thereto.

161. The TCR or antigen-binding fragment thereof of claim 158, wherein the peptide epitope is or comprises E7(11-19) YMLDLQPET (SEQ ID NO:

271).

162. The TCR or antigen-binding fragment thereof of claim 158, wherein:

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

47 and 60, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

77 and 88, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

103 and 114, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

126 and 137, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

149 and 157, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

169 and 180, respectively;

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

195 and 206, respectively;

or

the Vα and

Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

221 and 232, respectively.

163. The TCR or antigen-binding fragment thereof of claim 158, wherein the alpha chain further comprises an alpha constant (Cα

) region and the beta chain further comprises a beta constant (Cβ

) region.

164. The TCR or antigen-binding fragment thereof of claim 163, wherein the Cα

and Cβ

regions are mouse constant regions.

165. The TCR or antigen-binding fragment thereof of claim 163, wherein the Cα

and Cβ

regions are human constant regions.

166. The TCR or antigen-binding fragment thereof of claim 163 wherein the Cα

and/or Cβ

regions comprise one or more amino acid replacements to introduce one or more cysteine residues capable of forming one or more non-native disulfide bridges between the alpha chain and beta chain.

167. The TCR or antigen-binding fragment thereof of claim 163, wherein:

a) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

44, 74, 100, 123, 146, 166, 192, or 218, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

57, 85, 111, 134, 154, 177, 203, or 229, or a sequence of amino acids that has at least 90% sequence identity thereto;

b) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

44 and 57, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

74 and 85, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

100 and 111, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

123 and 134, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

146 and 154, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

166 and 177, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

192 and 202, respectively;

or the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

218 and 229, respectively;

c) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

43, 73, 99, 122, 145, 165, 191, or 217, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

56, 84, 110, 133, 153, 176, 202, or 228, or a sequence of amino acids that has at least 90% sequence identity thereto;

d) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

43 and 56, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

73 and 84, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

99 and 110, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

122 and 133, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

145 and 153, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

165 and 176, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

191 and 202, respectively;

or the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

217 and 228, respectively;

e) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

43, 73, 99, 122, 145, 165, 191, or 217, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

359, 370, 371, 372, 373, 374, 375 or 376, or a sequence of amino acids that has at least 90% sequence identity thereto;

or

f) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

43 and 359, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

73 and 370, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

99 and 371, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

122 and 372, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

145 and 373, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

165 and 374, respectively;

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

191 and 375, respectively;

or the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

217 and 376, respectively.

168. The TCR or antigen-binding fragment thereof of claim 158, that is human.

169. The TCR or antigen-binding fragment thereof of claim 158, wherein the antigen-specificity is at least partially CD8-independent.

170. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 158, or an alpha or a beta chain thereof.

171. A vector comprising the nucleic acid of claim 170.

172. An engineered cell comprising the nucleic acid molecule of claim 170.

173. An engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 158.

174. The engineered cell of claim 173, wherein the cell is a T cell.

175. A method for producing a cell expressing a recombinant TCR or antigen-binding fragment thereof, comprising introducing the vector of claim 171 into a cell.

176. A composition comprising engineered cells of claim 173.

177. The composition of claim 176, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

178. A method of treatment, comprising administering the composition of claim 176 to a subject having a disease or disorder associated with HPV.

160. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Va) region and a beta chain comprising a variable beta (Vβ

) region, wherein;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

47 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

60, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

77 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

88, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

103 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

114, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

126 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

137, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

149 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

157, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

169 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

180, or an amino acid sequence that has at least 90% sequence identity thereto;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

195 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

206, or an amino acid sequence that has at least 90% sequence identity thereto;

or

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

221 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

232, or an amino acid sequence that has at least 90% sequence identity thereto.

179. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E6 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Va) region and a beta chain comprising a variable beta (Vβ

) region, wherein;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

248, 249, and 250, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

259, 260, and 261, respectively.

180. The TCR or antigen-binding fragment thereof of claim 179, wherein:

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

247 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

258 or an amino acid sequence that has at least 90% sequence identity thereto.

182. The TCR or antigen-binding fragment thereof of claim 179, wherein the peptide epitope is or comprises E6(29-38) TIHDIILECV (SEQ ID NO:

268).

183. The TCR or antigen-binding fragment thereof of claim 179, wherein the Vα

and Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

247 and 258, respectively.

184. The TCR or antigen-binding fragment thereof of claim 179, wherein the alpha chain further comprises an alpha constant (Cα

) region and the beta chain further comprises a beta constant (Cβ

) region.

185. The TCR or antigen-binding fragment thereof of claim 184, wherein the Cα

and Cβ

regions are mouse constant regions.

186. The TCR or antigen-binding fragment thereof of claim 184, wherein the Cα

and Cβ

regions are human constant regions.

187. The TCR or antigen-binding fragment thereof of claim 184, wherein the Cα

and/or Cβ

regions comprise one or more amino acid replacements of one or more cysteine residues capable of forming one or more non-native disulfide bridges between the alpha chain and beta chain.

188. The TCR or antigen-binding fragment thereof of claim 184, wherein:

a) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

244, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

255, or a sequence of amino acids that has at least 90% sequence identity thereto;

b) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

244 and 255, respectively;

c) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

243, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

254, or a sequence of amino acids that has at least 90% sequence identity thereto;

d) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

243 and 254, respectively;

e) the alpha chain comprises the amino acid sequence set forth in SEQ ID NO;

243, or a sequence of amino acids that has at least 90% sequence identity thereto, and the beta chain comprises the amino acid sequence set forth in SEQ ID NO;

377, or a sequence of amino acids that has at least 90% sequence identity thereto;

or

f) the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs;

243 and 377, respectively.

189. The TCR or antigen-binding fragment thereof of claim 179, that is human.

190. The TCR or antigen-binding fragment thereof of claim 179, wherein the antigen-specificity is at least partially CD8-independent.

191. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 179, or an alpha or a beta chain thereof.

192. A vector comprising the nucleic acid of claim 191.

193. An engineered cell comprising the nucleic acid molecule of claim 191.

194. An engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 179.

195. The engineered cell of claim 194, wherein the cell is a T cell.

196. A method for producing a cell expressing a recombinant TCR or antigen-binding fragment thereof, comprising introducing the vector of claim 192 into a cell.

197. A composition comprising engineered cells of claim 194.

198. The composition of claim 197, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

199. A method of treatment, comprising administering the composition of claim 197 to a subject having a disease or disorder associated with HPV.

181. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E6 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Va) region and a beta chain comprising a variable beta (Vβ

) region, wherein;

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

247 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

258 or an amino acid sequence that has at least 90% sequence identity thereto.

200. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof, comprising an alpha chain comprising a variable alpha (Va) region and a beta chain comprising a variable beta (Vβ

) region, wherein;

the Vα

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

10, 11, and 12, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

25, 26, and 27, respectively.

201. The TCR or antigen-binding fragment thereof of claim 200, wherein:

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

9 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

24 or an amino acid sequence that has at least 90% sequence identity thereto.

202. The TCR or antigen-binding fragment thereof of claim 200, wherein the alpha chain further comprises an alpha constant (Cα

) region and the beta chain further comprises a beta constant (Cβ

) region.

203. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 200, or an alpha or a beta chain thereof.

204. A vector comprising the nucleic acid of claim 203.

205. An engineered cell comprising the nucleic acid molecule of claim 203.

206. An engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 200.

207. The engineered cell of claim 206, wherein the cell is a T cell.

208. A method for producing an engineered cell expressing a recombinant TCR or antigen-binding fragment, comprising introducing the vector of claim 204 into a cell.

209. A composition comprising engineered cells of claim 206.

210. A method of treatment, comprising administering the composition of claim 209 to a subject having a disease or disorder associated with HPV.